/ 
NBI-Slurm-0.6.2
⭐ Starred 1 / README.md

New Batch Interface for SLURM

.github/workflows/main.yml MetaCpan testers

Scripts

lsjobs

List or delete your jobs in the queue with lsjobs. By default search is restricted to the active user, which can be changed with -u USER or set to -u all.

See docs

lsjobs [options] [jobid.. | pattern ]

Add -d to delete the jobs (you will be prompted for confirmation).

lsjobs

runjob

Submit a job to the queue (with cores, memory, time, etc) with runjob.

See docs

runjob -n "my-job" -t 2 -r -c 18 -m 32 --after "python script.py --threads 18"

If invoked without --run (or -r) it will print the command to be executed.

runjob

waitjobs

Wait for all jobs matching a pattern to finish (to be used to run a second job when they are all finished), with waitjobs. You can send it to the queue, and use its JOBID as dependency for other jobs.

See docs

waitjobs [-u $USER] [pattern]

session

Start an interactive session with session, defaults can be saved in the configuration file.

See docs

session [-t 2 -c 18 -m 32]

whojobs

Who is using the cluster: list usernames and number of jobs in ascending order with whojobs. See docs

whojobs [--min-jobs INT]

whojobs

shelf

List packages installed in the NBI HPC with shelf. See docs

shelf QUERY_STRING

shelf

Configuration

The scripts will look for a configuration file in ~/.nbislurm.config where you can store your email address, default queue, and other options, as well as default parameters for interactive sessions. See the docs.

Perl Module

NBI::Slurm is a Perl package that provides a convenient interface for submitting jobs to SLURM, a workload manager for High-Performance Computing (HPC) clusters. It includes two main classes to submit jobs to SLURM:

And two classes to manage the output of the jobs:

Features

Installation

To use NBI::Slurm, you need Perl 5.12 or higher installed on your system. You can install the package using CPAN or manually by copying the NBI/Slurm.pm file to your Perl library directory.

cpanm is a command line utility for installing Perl modules from CPAN.

To install cpanm, run the following command:

# If you dont have cpanm installed:
curl -L https://cpanmin.us | perl - --sudo App::cpanminus

# Install with cpanm
cpanm NBI::Slurm

Library Usage

Here's a simple example demonstrating how to use NBI::Slurm to submit a job to SLURM:

use NBI::Job;
use NBI::Opts;

# Create a job
my $job = NBI::Job->new(
    -name    => "job-name",
    -command => "ls -l",
);

# Create options
my $opts = NBI::Opts->new(
    -queue   => "short",
    -threads => 4,
    -memory  => 8,
    -opts    => ["-m afterok:1234"],
);

# Set options for the job
$job->set_opts($opts);

# Submit the job to SLURM
my $jobid = $job->run;

For more detailed information on the available methods and options, please refer to the individual documentation of the NBI::Job and NBI::Opts classes.

Author

NBI::Slurm is written by Andrea Telatin

License

This module is released under the MIT License.